root/galaxy-central/eggs/bx_python-0.5.0_dev_f74aec067563-py2.6-macosx-10.6-universal-ucs2.egg/EGG-INFO/scripts/bed_count_overlapping.py @ 3

#!/usr/bin/python2.6
"""
For each interval in `bed1` count the number of intersecting regions in `bed2`.

usage: %prog bed1 bed2 
"""

import sys
from bx.intervals import *

bed1,bed2 = sys.argv[1:3]

ranges = {}
for line in open( bed2 ):
    fields = line.strip().split() 
    chrom, start, end, = fields[0], int(fields[1]), int(fields[2])
    if chrom not in ranges: ranges[chrom] = Intersecter()
    ranges[chrom].add_interval( Interval( start, end ) )
    
for line in open( bed1 ):
    fields = line.strip().split() 
    chrom, start, end = fields[0], int(fields[1]), int(fields[2]) 
    other = " ".join(fields[3:])
    out = " ".join(fields[:3] +[other])
    if chrom in ranges: 
        print out, len( ranges[chrom].find( start, end ) )
    else:
        print out, 0